yes, the pial and white surfaces have the same number of vertices and
they have the same identities
On 2/11/2021 1:25 PM, Krieger, Donald N. wrote:
External Email - Use Caution
It looks like your first answer, i.e. use of mri_annotation2label to
extract pial labels almost gets me there. I see that the pial and
white labels have exactly the same number and values for their
indices. Does this mean I can use the distance between the white and
pial vertex with the same label as a cortical thickness?
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Krieger, Donald N.
*Sent:* Thursday, February 11, 2021 1:16 PM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] cortical thickness values for each point
in a ctx label file
* External Email - Use Caution *
Thanks for getting back so quickly, Doug.
Creating pial label files will enable me to write something which does
what I want.
What I want to do is generate a list of cortical thickness values, one
for each vertex in a ctx label file. The main question is whether
something to do this has already been implemented in freesurfer. If
not, I will generate pial label files and then for each vertex in a
ctx label file, I will find the nearest points in that ROI’s pial and
white label files and use the sum of the two distances as the cortical
thickness.
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> *On Behalf Of
*Douglas N. Greve
*Sent:* Thursday, February 11, 2021 1:04 PM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] cortical thickness values for each point
in a ctx label file
Not sure what you mean as the pial files are surfaces not labels or
annotations. If you want to extract labels from the annotations you
can use mri_annotation2label
On 2/11/2021 12:55 PM, Krieger, Donald N. wrote:
* External Email - Use Caution *
Dear freesurfer group,
I wish to measure a cortical thickness value for each entry in a
label file, e.g. SubNo/wmparc/ctx-lh-lateraloccipital_1011.label .
Is there a function in the freesurfer distribution which includes
this capability?
Also, is there a function in the distribution that produces
regional label files from the surf/[lr]h.pial files?
Thanks - Don
Don Krieger, Ph.D.
Research Scientist
Department of Neurological Surgery
University of Pittsburgh
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